By DAVID E. SANGER

Published: February 8, 2004

WASHINGTON—
PLACE side by side the two intelligence problems that captivated Washington last week -- Iraq and Pakistan -- and you can see stunning, polar-opposite images of what happens when murky intelligence collides with political agendas.

The story of what happened to the prewar intelligence estimates of Iraq's weapons of mass destruction has already been endlessly picked apart, spun and turned to campaign fodder as members of President Bush's cabinet backpedal from the definitive declarations made a year ago. Now the politically crucial part of the mystery -- whether America's intelligence agencies misconnected the dots or whether President Bush and his team cherry-picked the evidence and ignored the caveats to justify a war they felt needed to be fought -- is falling into the lap of a commission that will report back well after the presidential election.

''Some prewar intelligence assessments by America and other nations about Iraq's weapon stockpiles have not been confirmed,'' Mr. Bush said Friday. ''We are determined to figure out why.''

But no one at the White House will say if the commission will examine the equally critical question of whether the administration moved fast enough as the Central Intelligence Agency slowly untangled the nuclear empire of Abdul Qadeer Khan, the father of the Pakistani nuclear bomb. As much as Mr. Bush's team wanted to topple Saddam Hussein in Iraq, they wanted to stabilize Pakistan's president, Gen. Pervez Musharraf, who many experts, from Washington to Islamabad, strongly suspected was turning a blind eye to how Dr. Khan was helping to arm some of the world's most hostile states.

The other burning question in Washington is whether the United States, because it needed Mr. Musharraf's help against Al Qaeda, waited too long to stop Dr. Khan's network as it traded in nuclear secrets and equipment. ''We didn't ignore the evidence -- far from it,'' one senior proliferation expert inside the administration said. ''But a decision was made not to trumpet it, either,'' for fear of destabilizing Mr. Musharraf and ending up with an extreme Islamic government with a nuclear arsenal.

To many intelligence experts in Washington, Mr. Khan was a threat far more urgent and imminent than Mr. Hussein. For 15 years he peddled his recipes, and the equipment to do the mixing, to the highest bidders. There were many takers: Iran, North Korea, Libya and probably customers whose names have not surfaced yet. ''He's the real-life Dr. No,'' a senior American intelligence official said the other day, referring to the evil antagonist of James Bond lore. ''Only more terrifying.''

After years of denials, his own and the Pakistani government's, Dr. Khan finally confessed last week. George J. Tenet, the director of central intelligence, portrayed the unmasking of the Khan operation as a brilliant act of American spycraft. He said the C.I.A. had been tracking Dr. Khan for years, which is true.

But as in Iraq, the story of the intelligence is more complex, a puzzle whose pieces were scattered around the globe. Many were not found until the damage had been done. ''We knew he was trading in missiles, and suspected he was getting into the nuclear business as well,'' Gary Samore, the head of nonproliferation in the Clinton Administration's national security council, recalled not long ago. ''But I don't think we knew he was the supplier for Iran's program.'' Or for Libya's, a fact that emerged over the past year or so, and was not confirmed until inspectors sent bomb designs -- for a Pakistani adaptation of a Chinese design -- back to Washington two weeks ago.

And as with Iraq, a critical question is how intelligence was put to use. In his efforts to stem proliferation, Mr. Bush has threatened sanctions against Iran and Libya. He demanded that North Korea accept inspections. But General Musharraf has been allowed to play by different rules.

Few of Mr. Bush's aides believe Pakistan's story that Dr. Khan operated alone. He has the deepest ties to the military, which oversaw the Khan Research Laboratories, and supplied it with a cargo fleet. Pakistan got missiles from North Korea, investigators believe, in return for uranium enrichment technology. Clearly, the Pakistani government must have known something about how its new missile fleet materialized.

But when Mr. Musharraf struck a deal last week with Dr. Khan -- a televised apology that absolved the government, in return for a full pardon -- the White House applauded Mr. Musharraf. When the Pakistani president dismissed as ''rubbish'' calls that he investigate the military's role, the White House said nothing. In fact, when President Bush on Friday named the members of the intelligence commission, asking them to examine troubles in penetrating countries whose weapons, ambitions or links to terrorism pose a threat to America, he named Iran, Libya, Afghanistan. Pakistan was not on the list.

''Look, it seems Machiavellian, but it is Machiavelli with a purpose,'' said George Perkovich, a Pakistan expert at the Carnegie Endowment for International Peace. ''It's worth it if you are secretly getting enough cooperation from the Pakistanis to map the entire enterprise and roll it up. But there's always the possibility that you are being played by Pakistan: that they will give you just enough information to keep the money flowing, but not enough to root out the real problem.''

On Friday, Secretary of State Colin L. Powell said he would remind General Musharraf that the United States needs ''a full understanding of what the A.Q. Khan network has done over the years so that there are no remnants of it left.'' But it is Mr. Musharraf who assured Mr. Powell 16 months ago -- after The New York Times revealed that American intelligence had concluded that Pakistan supplied nuclear technology to North Korea, apparently in exchange for missiles -- that any such activities were in the past. Exchanges with Libya occurred as recently as five months ago.

Administration officials say Mr. Musharraf went as far as he could, and that even now he is being tarred by the opposition as a yes-man to America. But one risk is that other nations will conclude that if you are a valuable enough ally to the United States, the usual nuclear rules will be waived.

Another risk, notes Michael Krepon, the president of the Henry L. Stimson Center, which works on security issues, is that other nations ''could adopt the Pakistani definition of proliferation: If the state needs to swap some nuclear technology to modernize its deterrent, that's defense, not proliferation.''

It's a distinction that no one in the White House wants to discuss.

Photo: In 1998, Dr. Abdul Qadeer Khan, father of Pakistan's nuclear bomb, was honored by the government. (Photo by Associated Press)